Updates

jblindsay · Jul 13, 2022 · cbd2c3c · cbd2c3c
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
diff --git a/.vscode/launch.json b/.vscode/launch.json
diff --git a/.vscode/settings.json b/.vscode/settings.json
diff --git a/.vscode/tasks.json b/.vscode/tasks.json
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
diff --git a/LICENSE.txt b/LICENSE.txt
diff --git a/README.md b/README.md
diff --git a/UserManual.txt b/UserManual.txt
diff --git a/build.py b/build.py
diff --git a/doc_img/ArcGIS_toolbox.png b/doc_img/ArcGIS_toolbox.png
diff --git a/doc_img/AssessRoute_avg_slope.png b/doc_img/AssessRoute_avg_slope.png
diff --git a/doc_img/AssessRoute_visibility.png b/doc_img/AssessRoute_visibility.png
diff --git a/doc_img/DSM.png b/doc_img/DSM.png
diff --git a/doc_img/FeaturePreservingSmoothing_fig1.png b/doc_img/FeaturePreservingSmoothing_fig1.png
diff --git a/doc_img/FeaturePreservingSmoothing_fig2.png b/doc_img/FeaturePreservingSmoothing_fig2.png
diff --git a/doc_img/FirstReturnTIN.png b/doc_img/FirstReturnTIN.png
diff --git a/doc_img/GHRGLogoSm.png b/doc_img/GHRGLogoSm.png
diff --git a/doc_img/Geomorphons.jpg b/doc_img/Geomorphons.jpg
diff --git a/doc_img/HorizonAngle.png b/doc_img/HorizonAngle.png
diff --git a/doc_img/HypsometricAnalysis_fig1.png b/doc_img/HypsometricAnalysis_fig1.png
diff --git a/doc_img/LidarHistogram_fig1.png b/doc_img/LidarHistogram_fig1.png
diff --git a/doc_img/LidarSegmentation.png b/doc_img/LidarSegmentation.png
diff --git a/doc_img/MaxBranchLength_fig1.png b/doc_img/MaxBranchLength_fig1.png
diff --git a/doc_img/MultidirectionalHillshade_fig1.png b/doc_img/MultidirectionalHillshade_fig1.png
diff --git a/doc_img/MultidirectionalHillshade_fig2.png b/doc_img/MultidirectionalHillshade_fig2.png
diff --git a/doc_img/MultidirectionalHillshade_fig3.png b/doc_img/MultidirectionalHillshade_fig3.png
diff --git a/doc_img/QGIS_add_repo.png b/doc_img/QGIS_add_repo.png
diff --git a/doc_img/QGIS_plugin.png b/doc_img/QGIS_plugin.png
diff --git a/doc_img/QGIS_settings.png b/doc_img/QGIS_settings.png
diff --git a/doc_img/QGIS_whitebox.png b/doc_img/QGIS_whitebox.png
diff --git a/doc_img/SlopeVsElevationPlot_fig1.png b/doc_img/SlopeVsElevationPlot_fig1.png
diff --git a/doc_img/StElis_point_cloud.png b/doc_img/StElis_point_cloud.png
diff --git a/doc_img/StochasticDepressionAnalysis_fig1.png b/doc_img/StochasticDepressionAnalysis_fig1.png
diff --git a/doc_img/TimeInDaylight.png b/doc_img/TimeInDaylight.png
diff --git a/doc_img/VisiibilityIndex_fig1.png b/doc_img/VisiibilityIndex_fig1.png
diff --git a/doc_img/WBRunner.png b/doc_img/WBRunner.png
diff --git a/doc_img/WhiteboxToolsLogoBlue.png b/doc_img/WhiteboxToolsLogoBlue.png
diff --git a/doc_img/WhiteboxToolsLogo_vert.svg b/doc_img/WhiteboxToolsLogo_vert.svg
diff --git a/doc_img/example_project_dir.png b/doc_img/example_project_dir.png
diff --git a/doc_img/flow_accum.png b/doc_img/flow_accum.png
diff --git a/doc_img/hypsometricallyTintedHillshade_fig1.png b/doc_img/hypsometricallyTintedHillshade_fig1.png
diff --git a/doc_img/wbt_auotcomplete.png b/doc_img/wbt_auotcomplete.png
diff --git a/doc_img/wbt_directory.png b/doc_img/wbt_directory.png
diff --git a/img/.DS_Store b/img/.DS_Store
diff --git a/img/WBRunner.png b/img/WBRunner.png
diff --git a/img/WhiteboxToolsLogo.png b/img/WhiteboxToolsLogo.png
diff --git a/img/WhiteboxToolsLogo.svg b/img/WhiteboxToolsLogo.svg
diff --git a/img/WhiteboxToolsLogoBlue.png b/img/WhiteboxToolsLogoBlue.png
diff --git a/img/WhiteboxToolsLogoGreen.png b/img/WhiteboxToolsLogoGreen.png
diff --git a/img/WhiteboxToolsLogo_box_only.svg b/img/WhiteboxToolsLogo_box_only.svg
diff --git a/img/WhiteboxToolsLogo_vert.svg b/img/WhiteboxToolsLogo_vert.svg
diff --git a/img/WhiteboxToolsLogo_vert1.png b/img/WhiteboxToolsLogo_vert1.png
diff --git a/img/WhiteboxToolsLogo_vert2.png b/img/WhiteboxToolsLogo_vert2.png
diff --git a/img/WhiteboxToolsLogo_vert3.png b/img/WhiteboxToolsLogo_vert3.png
diff --git a/img/WhiteboxToolsLogo_vert4.png b/img/WhiteboxToolsLogo_vert4.png
diff --git a/img/closed.gif b/img/closed.gif
diff --git a/img/closed.png b/img/closed.png
diff --git a/img/open.gif b/img/open.gif
diff --git a/img/open.png b/img/open.png
diff --git a/img/tool.gif b/img/tool.gif
diff --git a/img/tool.png b/img/tool.png
diff --git a/readme.txt b/readme.txt
@@ -57,16 +57,18 @@ for more details.
 ******************
 Version 2.X.X (XX-XX-20XX)
 - Added the TravellingSalesmanProblem tool for identifying short routes connecting multiple locations.
+- Added the HeatMap tool for performing kernel density estimation (KDE) from vector points.
 - Added the MultiplyOverlay tool.
 - Added the MaxUpslopeValue tool.
 - Fixed a bug in the automatic install of the Whitebox extensions that affected Windows users.
 - Fixed a bug with the persistence of the compress_rasters parameter. Python users were unable to
   turn off the compress flag previously.
-- Added the ability to set and get the maximum number of processors (--max_procs flag) used by WBT in 
+- Added the option to set and get the maximum number of processors (--max_procs flag) used by WBT in 
   the Whitebox Python API.
-- Added the ability to output average point density and nominal point spacing to the LidarInfo tool.
+- Added the option to output average point density and nominal point spacing to the LidarInfo tool.
 - Updated the ClassifyOverlapPoints and FlightlineOverlap tools to use information contained within
-  the Point Source ID property, rather than a hard-coded time difference threshold, as previously used.
+  the Point Source ID property, rather than a hard-coded time difference threshold previously used.
+- Fixed an issue that affected many tools when input rasters use either NaN or Inf as NoData values.
 
 Version 2.1.0 (30-01-2022)
 - The Geomorphons tool for landform classification is now available.

diff --git a/tool_porting.md b/tool_porting.md
diff --git a/wb_runner.py b/wb_runner.py
@@ -1106,7 +1106,7 @@ def update_tool_help(self):
                 b.grid(row=param_num, column=0, sticky=tk.W)
                 param_num = param_num + 1
             elif ('Float' in pt or 'Integer' in pt or
-                  'String' in pt or 'StringOrNumber' in pt or
+                  'Text' in pt or 'String' in pt or 'StringOrNumber' in pt or
                   'StringList' in pt or 'VectorAttributeField' in pt):
                 b = DataInput(json_str, self.arg_scroll_frame)
                 b.grid(row=param_num, column=0, sticky=tk.NSEW)

diff --git a/whitebox-common/Cargo.lock b/whitebox-common/Cargo.lock
diff --git a/whitebox-common/Cargo.toml b/whitebox-common/Cargo.toml
diff --git a/whitebox-common/build.rs b/whitebox-common/build.rs
diff --git a/whitebox-common/src/algorithms/convex_hull.rs b/whitebox-common/src/algorithms/convex_hull.rs
diff --git a/whitebox-common/src/algorithms/delaunay_triangulation.rs b/whitebox-common/src/algorithms/delaunay_triangulation.rs
diff --git a/whitebox-common/src/algorithms/is_clockwise_order.rs b/whitebox-common/src/algorithms/is_clockwise_order.rs
diff --git a/whitebox-common/src/algorithms/line_ops.rs b/whitebox-common/src/algorithms/line_ops.rs
diff --git a/whitebox-common/src/algorithms/lzw.rs b/whitebox-common/src/algorithms/lzw.rs
diff --git a/whitebox-common/src/algorithms/minimum_bounding_box.rs b/whitebox-common/src/algorithms/minimum_bounding_box.rs
diff --git a/whitebox-common/src/algorithms/mod.rs b/whitebox-common/src/algorithms/mod.rs
diff --git a/whitebox-common/src/algorithms/poly_area.rs b/whitebox-common/src/algorithms/poly_area.rs
diff --git a/whitebox-common/src/algorithms/poly_ops.rs b/whitebox-common/src/algorithms/poly_ops.rs
diff --git a/whitebox-common/src/algorithms/poly_perimeter.rs b/whitebox-common/src/algorithms/poly_perimeter.rs
diff --git a/whitebox-common/src/algorithms/smallest_enclosing_circle.rs b/whitebox-common/src/algorithms/smallest_enclosing_circle.rs
diff --git a/whitebox-common/src/configs/mod.rs b/whitebox-common/src/configs/mod.rs
diff --git a/whitebox-common/src/lib.rs b/whitebox-common/src/lib.rs
diff --git a/whitebox-common/src/plugins.rs b/whitebox-common/src/plugins.rs
diff --git a/whitebox-common/src/rendering/box_whisker.rs b/whitebox-common/src/rendering/box_whisker.rs
diff --git a/whitebox-common/src/rendering/histogram.rs b/whitebox-common/src/rendering/histogram.rs
diff --git a/whitebox-common/src/rendering/html.rs b/whitebox-common/src/rendering/html.rs
diff --git a/whitebox-common/src/rendering/line_graph.rs b/whitebox-common/src/rendering/line_graph.rs
diff --git a/whitebox-common/src/rendering/mod.rs b/whitebox-common/src/rendering/mod.rs
diff --git a/whitebox-common/src/rendering/scattergram.rs b/whitebox-common/src/rendering/scattergram.rs
diff --git a/whitebox-common/src/spatial_ref_system/epsg_to_wkt.rs b/whitebox-common/src/spatial_ref_system/epsg_to_wkt.rs
diff --git a/whitebox-common/src/spatial_ref_system/mod.rs b/whitebox-common/src/spatial_ref_system/mod.rs
diff --git a/whitebox-common/src/structures/array2d.rs b/whitebox-common/src/structures/array2d.rs
diff --git a/whitebox-common/src/structures/bounding_box.rs b/whitebox-common/src/structures/bounding_box.rs
diff --git a/whitebox-common/src/structures/circle.rs b/whitebox-common/src/structures/circle.rs
diff --git a/whitebox-common/src/structures/fixed_radius_search.rs b/whitebox-common/src/structures/fixed_radius_search.rs
diff --git a/whitebox-common/src/structures/line_segment.rs b/whitebox-common/src/structures/line_segment.rs
diff --git a/whitebox-common/src/structures/mod.rs b/whitebox-common/src/structures/mod.rs
diff --git a/whitebox-common/src/structures/n_maximizer.rs b/whitebox-common/src/structures/n_maximizer.rs
diff --git a/whitebox-common/src/structures/n_minimizer.rs b/whitebox-common/src/structures/n_minimizer.rs
diff --git a/whitebox-common/src/structures/point2d.rs b/whitebox-common/src/structures/point2d.rs
diff --git a/whitebox-common/src/structures/point3d.rs b/whitebox-common/src/structures/point3d.rs
diff --git a/whitebox-common/src/structures/polyline.rs b/whitebox-common/src/structures/polyline.rs
diff --git a/whitebox-common/src/structures/polynomial_regression_2d.rs b/whitebox-common/src/structures/polynomial_regression_2d.rs
diff --git a/whitebox-common/src/structures/radial_basis_function.rs b/whitebox-common/src/structures/radial_basis_function.rs
diff --git a/whitebox-common/src/structures/rectangle_with_data.rs b/whitebox-common/src/structures/rectangle_with_data.rs
diff --git a/whitebox-common/src/utils/byte_order_reader.rs b/whitebox-common/src/utils/byte_order_reader.rs
diff --git a/whitebox-common/src/utils/byte_order_writer.rs b/whitebox-common/src/utils/byte_order_writer.rs
diff --git a/whitebox-common/src/utils/mod.rs b/whitebox-common/src/utils/mod.rs
diff --git a/whitebox-lidar/Cargo.lock b/whitebox-lidar/Cargo.lock
diff --git a/whitebox-lidar/Cargo.toml b/whitebox-lidar/Cargo.toml
diff --git a/whitebox-lidar/src/header.rs b/whitebox-lidar/src/header.rs
diff --git a/whitebox-lidar/src/las.rs b/whitebox-lidar/src/las.rs
@@ -468,7 +468,7 @@ impl LasFile {
     }
 
     pub fn get_rgb(&self, index: usize) -> Result<ColourData, Error> {
-        if self.colour_data.len() >= index {
+        if self.colour_data.len() > index {
             return Ok(self.colour_data[index]);
         } else {
             return Err(Error::new(ErrorKind::NotFound, "RGB value not found, possibly because the file point format does not include colour data."));
@@ -480,7 +480,7 @@ impl LasFile {
     }
 
     pub fn get_gps_time(&self, index: usize) -> Option<f64> { // Result<f64, Error> {
-        if self.gps_data.len() >= index {
+        if self.gps_data.len() > index {
             return Some(self.gps_data[index]); // Ok(self.gps_data[index]);
         // } else {
         //     return Err(Error::new(ErrorKind::NotFound, "GPS time value not found, possibly because the file point format does not include GPS data."));

diff --git a/whitebox-lidar/src/lib.rs b/whitebox-lidar/src/lib.rs
diff --git a/whitebox-lidar/src/point_data.rs b/whitebox-lidar/src/point_data.rs
diff --git a/whitebox-lidar/src/vlr.rs b/whitebox-lidar/src/vlr.rs
diff --git a/whitebox-lidar/src/zlidar_compression.rs b/whitebox-lidar/src/zlidar_compression.rs
diff --git a/whitebox-plugins/.DS_Store b/whitebox-plugins/.DS_Store
diff --git a/whitebox-plugins/Cargo.toml b/whitebox-plugins/Cargo.toml
@@ -20,6 +20,10 @@ path = "src/exposure_towards_wind_flux/main.rs"
 name = "gaussian_scale_space"
 path = "src/gaussian_scale_space/main.rs"
 
+[[bin]]
+name = "heat_map"
+path = "src/heat_map/main.rs"
+
 [[bin]]
 name = "lidar_shift"
 path = "src/lidar_shift/main.rs"
@@ -58,10 +62,12 @@ path = "src/travelling_salesman_problem/main.rs"
 
 [dependencies]
 fasteval = "0.2.4"
+kd-tree = "0.4.1"
 nalgebra = "0.18.0"
 num_cpus = "1.13.0"
 rand = { version = "0.7", features = ["small_rng"] }
 tsp-rs = "0.1.0"
+typenum = "1.15.0"
 whitebox_common = { path = "../whitebox-common" }
 whitebox_lidar = { path = "../whitebox-lidar" }
 whitebox_raster = { path = "../whitebox-raster" }

diff --git a/whitebox-plugins/src/.DS_Store b/whitebox-plugins/src/.DS_Store
diff --git a/whitebox-plugins/src/conditional_evaluation/conditional_evaluation.json b/whitebox-plugins/src/conditional_evaluation/conditional_evaluation.json
diff --git a/whitebox-plugins/src/conditional_evaluation/main.rs b/whitebox-plugins/src/conditional_evaluation/main.rs
diff --git a/whitebox-plugins/src/edge_contamination/edge_contamination.json b/whitebox-plugins/src/edge_contamination/edge_contamination.json
diff --git a/whitebox-plugins/src/edge_contamination/main.rs b/whitebox-plugins/src/edge_contamination/main.rs
diff --git a/whitebox-plugins/src/exposure_towards_wind_flux/exposure_towards_wind_flux.json b/whitebox-plugins/src/exposure_towards_wind_flux/exposure_towards_wind_flux.json
diff --git a/whitebox-plugins/src/exposure_towards_wind_flux/main.rs b/whitebox-plugins/src/exposure_towards_wind_flux/main.rs
diff --git a/whitebox-plugins/src/gaussian_scale_space/gaussian_scale_space.json b/whitebox-plugins/src/gaussian_scale_space/gaussian_scale_space.json
diff --git a/whitebox-plugins/src/gaussian_scale_space/main.rs b/whitebox-plugins/src/gaussian_scale_space/main.rs
diff --git a/whitebox-plugins/src/heat_map/.DS_Store b/whitebox-plugins/src/heat_map/.DS_Store
diff --git a/whitebox-plugins/src/heat_map/heat_map.json b/whitebox-plugins/src/heat_map/heat_map.json
@@ -0,0 +1,66 @@
+{
+    "tool_name": "HeatMap",
+    "exe": "heat_map",
+    "short_description": "This tool calculates a heat map, or kernel density estimation (KDE), for an input point set.",
+    "toolbox": "GIS Analysis",
+    "license": "Proprietary",
+    "example": ">> .*EXE_NAME -r=HeatMap -i=points.shp -o=density.tif --bandwidth=1000.0 --kernel='quartic' --cell_size=10.0",
+    "parameters": [
+        {
+            "name": "Input Points",
+            "flags": ["-i", "--input"],
+            "description": "Name of the input points shapefile.",
+            "parameter_type": {"ExistingFile":{"Vector":"Point"}},
+            "default_value": null,
+            "optional": false
+        },
+        {
+            "name": "Weight Field Name (Optional)",
+            "flags": ["--weights", "--weight_field"],
+            "description": "Optional name of the attribute containing point weight.",
+            "parameter_type": "String",
+            "default_value": null,
+            "optional": true
+        },
+        {
+            "name": "Output Raster Image",
+            "flags": ["-o", "--output"],
+            "description": "Name of the output raster image file.",
+            "parameter_type": {"NewFile":"Raster"},
+            "default_value": null,
+            "optional": false
+        },
+        {
+            "name": "Bandwidth",
+            "flags": ["--bandwidth"],
+            "description": "Bandwidth (metres).",
+            "parameter_type": "Float",
+            "default_value": "",
+            "optional": false
+        },
+        {
+            "name": "Kernel Type",
+            "flags": ["--kernel"],
+            "description": "Kernel type; one of 'uniform', 'triangular', 'epanechnikov', 'quartic', 'triweight', 'tricube', 'gaussian', 'cosine', 'logistic', 'sigmoid', 'silverman'.",
+            "parameter_type": {"OptionList": ["uniform", "triangular", "epanechnikov", "quartic", "triweight", "tricube", "gaussian", "cosine", "logistic", "sigmoid", "silverman"]},
+            "default_value": "quartic",
+            "optional": true
+        },
+        {
+            "name": "Output Raster Cell Size (Optional)",
+            "flags": ["--cell_size"],
+            "description": "Optionally specified cell size of output raster, in metres. Not used when base raster is specified.",
+            "parameter_type": "Float",
+            "default_value": "",
+            "optional": true
+        },
+        {
+            "name": "Base Raster (Optional)",
+            "flags": ["--base"],
+            "description": "Optionally specified input base raster file. Not used when a cell size is specified.",
+            "parameter_type": {"ExistingFile":"Raster"},
+            "default_value": null,
+            "optional": true
+        }
+    ]
+}