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jblindsay · Jan 20, 2019 · 3609a99 · 3609a99
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diff --git a/README.md b/README.md
@@ -6,6 +6,8 @@
 
 *This page is related to the stand-alone command-line program and Python scripting API for geospatial analysis, **WhiteboxTools**. If you are instead interested in the open-source GIS, **Whitebox GAT**, please see this [link](https://github.com/jblindsay/whitebox-geospatial-analysis-tools).*
 
+The official WhiteboxTools User Manual can be found [at this link](https://jblindsay.github.io/wbt_book/index.html).
+
 **Contents**
 
 1. [Description](#1-description)

diff --git a/src/tools/gis_analysis/construct_vector_tin.rs b/src/tools/gis_analysis/construct_vector_tin.rs
@@ -18,7 +18,14 @@ use std::f64;
 use std::io::{Error, ErrorKind};
 use std::path;
 
-/// This tool creates a vector triangular irregular network (TIN) for a set of vector points.
+/// This tool creates a vector triangular irregular network (TIN) for a set of vector points (`--input`)
+/// using a 2D [Delaunay triangulation](https://en.wikipedia.org/wiki/Delaunay_triangulation) algorithm.
+/// TIN vertex heights can be assigned based on either a field in the vector's attribute table (`--field`),
+/// or alternatively, if the vector is of a z-dimension *ShapeTypeDimension*, the point z-values may be
+/// used for vertex heights (`--use_z`). For LiDAR points, use the `LidarConstructVectorTIN` tool instead.
+/// 
+/// # See Also
+/// `LidarConstructVectorTIN`
 pub struct ConstructVectorTIN {
     name: String,
     description: String,

diff --git a/src/tools/gis_analysis/create_hexagonal_vector_grid.rs b/src/tools/gis_analysis/create_hexagonal_vector_grid.rs
@@ -2,7 +2,7 @@
 This tool is part of the WhiteboxTools geospatial analysis library.
 Authors: Dr. John Lindsay
 Created: 15/09/2018
-Last Modified: 13/10/2018
+Last Modified: 20/01/2019
 License: MIT
 */
 
@@ -19,8 +19,11 @@ use std::path;
 
 /// This tool can be used to create a hexagonal vector grid. The extent of the hexagonal
 /// grid is based on the extent of a user-specified base file (any supported raster format,
-/// shapefiles, or LAS files). The user must also specify the origin of the grid (x and y
-/// coordinates) and the hexagonal cell width.
+/// shapefiles, or LAS files). The user must also specify the hexagonal cell width (`--width`) 
+/// and whether the hexagonal orientation (`--orientation`) is `horizontal` or `vertical`.
+/// 
+/// # See Also
+/// `CreateRectangularVectorGrid`
 pub struct CreateHexagonalVectorGrid {
     name: String,
     description: String,
@@ -39,7 +42,7 @@ impl CreateHexagonalVectorGrid {
         let mut parameters = vec![];
         parameters.push(ToolParameter {
             name: "Input Base File".to_owned(),
-            flags: vec!["-i".to_owned(), "--input".to_owned()],
+            flags: vec!["-i".to_owned(), "--base".to_owned(), "--input".to_owned()],
             description: "Input base file.".to_owned(),
             parameter_type: ParameterType::ExistingFile(ParameterFileType::RasterAndVector(
                 VectorGeometryType::Any,
@@ -169,7 +172,7 @@ impl WhiteboxTool for CreateHexagonalVectorGrid {
                 keyval = true;
             }
             let flag_val = vec[0].to_lowercase().replace("--", "-");
-            if flag_val == "-i" || flag_val == "-input" {
+            if flag_val == "-i" || flag_val == "-input" || flag_val == "-base" {
                 input_file = if keyval {
                     vec[1].to_string()
                 } else {

diff --git a/src/tools/gis_analysis/create_rectangular_vector_grid.rs b/src/tools/gis_analysis/create_rectangular_vector_grid.rs
@@ -2,7 +2,7 @@
 This tool is part of the WhiteboxTools geospatial analysis library.
 Authors: Dr. John Lindsay
 Created: 15/09/2018
-Last Modified: 13/10/2018
+Last Modified: 20/01/2019
 License: MIT
 */
 
@@ -19,8 +19,11 @@ use std::path;
 
 /// This tool can be used to create a rectangular vector grid. The extent of the rectangular
 /// grid is based on the extent of a user-specified base file (any supported raster format,
-/// shapefiles, or LAS files). The user must also specify the origin of the grid (x and y
-/// coordinates) and the grid cell width and height.
+/// shapefiles, or LAS files). The user must also specify the origin of the grid (`--xorig` 
+/// and `--yorig`) and the grid cell width and height (`--width` and `--height`).
+/// 
+/// # See Also
+/// `CreateHexagonalVectorGrid`
 pub struct CreateRectangularVectorGrid {
     name: String,
     description: String,
@@ -39,7 +42,7 @@ impl CreateRectangularVectorGrid {
         let mut parameters = vec![];
         parameters.push(ToolParameter {
             name: "Input Base File".to_owned(),
-            flags: vec!["-i".to_owned(), "--input".to_owned()],
+            flags: vec!["-i".to_owned(), "--base".to_owned(), "--input".to_owned()],
             description: "Input base file.".to_owned(),
             parameter_type: ParameterType::ExistingFile(ParameterFileType::RasterAndVector(
                 VectorGeometryType::Any,
@@ -186,7 +189,7 @@ impl WhiteboxTool for CreateRectangularVectorGrid {
                 keyval = true;
             }
             let flag_val = vec[0].to_lowercase().replace("--", "-");
-            if flag_val == "-i" || flag_val == "-input" {
+            if flag_val == "-i" || flag_val == "-input" || flag_val == "-base" {
                 input_file = if keyval {
                     vec[1].to_string()
                 } else {

diff --git a/src/tools/hydro_analysis/average_flowpath_slope.rs b/src/tools/hydro_analysis/average_flowpath_slope.rs
@@ -350,7 +350,7 @@ impl WhiteboxTool for AverageFlowpathSlope {
         ];
         let (mut row, mut col): (isize, isize);
         let (mut row_n, mut col_n): (isize, isize);
-        let mut val: i64;
+        let mut val: i32;
         let mut dir: i8;
         let mut length: f64;
         let mut z_mean: f64;

diff --git a/src/tools/lidar_analysis/lidar_construct_vector_tin.rs b/src/tools/lidar_analysis/lidar_construct_vector_tin.rs
@@ -20,7 +20,16 @@ use std::sync::mpsc;
 use std::sync::{Arc, Mutex};
 use std::{env, f64, fs, path, thread};
 
-/// Creates a vector triangular irregular network (TIN) fitted to LiDAR points.
+/// This tool creates a vector triangular irregular network (TIN) for a set of LiDAR points (`--input`)
+/// using a 2D [Delaunay triangulation](https://en.wikipedia.org/wiki/Delaunay_triangulation) algorithm.
+/// LiDAR points may be excluded from the triangulation operation based on a number of criteria, 
+/// include the point return number (`--returns`), point classification value (`--exclude_cls`), or 
+/// a minimum (`--minz`) or maximum (`--maxz`) elevation. 
+/// 
+/// For vector points, use the `ConstructVectorTIN` tool instead. 
+/// 
+/// # See Also
+/// `ConstructVectorTIN`
 pub struct LidarConstructVectorTIN {
     name: String,
     description: String,

diff --git a/src/tools/lidar_analysis/lidar_elevation_slice.rs b/src/tools/lidar_analysis/lidar_elevation_slice.rs
@@ -1,8 +1,8 @@
 /*
 This tool is part of the WhiteboxTools geospatial analysis library.
 Authors: Dr. John Lindsay
-Created: June 2, 2017
-Last Modified: February 14, 2018
+Created: 02/06/2017
+Last Modified: 20/01/2019
 License: MIT
 */
 
@@ -13,6 +13,16 @@ use std::f64;
 use std::io::{Error, ErrorKind};
 use std::path;
 
+/// This tool can be used to either extract or classify the elevation values (z) of LiDAR points within 
+/// a specified elevation range (slice). In addition to the names of the input and output LiDAR files
+/// (`--input` and `--output`), the user must specify the lower (`--minz`) and upper (`--maxz`) bounds of 
+/// the elevation range. By default, the tool will only output points within the elevation slice, filtering
+/// out all points lying outside of this range. If the `--class` parameter is used, the tool will operate
+/// by assigning a class value (`--inclassval`) to the classification bit of points within the slice and
+/// another class value (`--outclassval`) to those points falling outside the range.
+/// 
+/// # See Also
+/// `LidarRemoveOutliers`, `LidarClassifySubset`
 pub struct LidarElevationSlice {
     name: String,
     description: String,
@@ -186,48 +196,45 @@ impl WhiteboxTool for LidarElevationSlice {
             if vec.len() > 1 {
                 keyval = true;
             }
-            if vec[0].to_lowercase() == "-i" || vec[0].to_lowercase() == "--input" {
-                if keyval {
-                    input_file = vec[1].to_string();
+            let flag_val = vec[0].to_lowercase().replace("--", "-");
+            if flag_val == "-i" || flag_val == "-input" {
+                input_file = if keyval {
+                    vec[1].to_string()
                 } else {
-                    input_file = args[i + 1].to_string();
-                }
-            } else if vec[0].to_lowercase() == "-o" || vec[0].to_lowercase() == "--output" {
-                if keyval {
-                    output_file = vec[1].to_string();
+                    args[i + 1].to_string()
+                };
+            } else if flag_val == "-o" || flag_val == "-output" {
+                output_file = if keyval {
+                    vec[1].to_string()
                 } else {
-                    output_file = args[i + 1].to_string();
-                }
-            } else if vec[0].to_lowercase() == "-maxz" || vec[0].to_lowercase() == "--maxz" {
-                if keyval {
-                    maxz = vec[1].to_string().parse::<f64>().unwrap();
+                    args[i + 1].to_string()
+                };
+            } else if flag_val == "-maxz" {
+                maxz = if keyval {
+                    vec[1].to_string().parse::<f64>().unwrap()
                 } else {
-                    maxz = args[i + 1].to_string().parse::<f64>().unwrap();
-                }
-            } else if vec[0].to_lowercase() == "-minz" || vec[0].to_lowercase() == "--minz" {
-                if keyval {
-                    minz = vec[1].to_string().parse::<f64>().unwrap();
+                    args[i + 1].to_string().parse::<f64>().unwrap()
+                };
+            } else if flag_val == "-minz" {
+                minz = if keyval {
+                    vec[1].to_string().parse::<f64>().unwrap()
                 } else {
-                    minz = args[i + 1].to_string().parse::<f64>().unwrap();
-                }
-            } else if vec[0].to_lowercase() == "-class" || vec[0].to_lowercase() == "--class" {
+                    args[i + 1].to_string().parse::<f64>().unwrap()
+                };
+            } else if flag_val == "-class" {
                 filter = false;
-            } else if vec[0].to_lowercase() == "-inclassval"
-                || vec[0].to_lowercase() == "--inclassval"
-            {
-                if keyval {
-                    in_class_value = vec[1].to_string().parse::<u8>().unwrap();
+            } else if flag_val == "-inclassval" {
+                in_class_value = if keyval {
+                    vec[1].to_string().parse::<u8>().unwrap()
                 } else {
-                    in_class_value = args[i + 1].to_string().parse::<u8>().unwrap();
-                }
-            } else if vec[0].to_lowercase() == "-outclassval"
-                || vec[0].to_lowercase() == "--outclassval"
-            {
-                if keyval {
-                    out_class_value = vec[1].to_string().parse::<u8>().unwrap();
+                    args[i + 1].to_string().parse::<u8>().unwrap()
+                };
+            } else if flag_val == "-outclassval" {
+                out_class_value = if keyval {
+                    vec[1].to_string().parse::<u8>().unwrap()
                 } else {
-                    out_class_value = args[i + 1].to_string().parse::<u8>().unwrap();
-                }
+                    args[i + 1].to_string().parse::<u8>().unwrap()
+                };
             }
         }