Merge csiro-internal and csiro-robotics mains

.devcontainer/Dockerfile

@@ -29,7 +29,6 @@ RUN apt-get update && apt-get upgrade -y && \
 # Clone, build and clean up LASzip (3.x supports LAS 1.4 via laszip_api.h C API)
 RUN git clone https://github.com/LASzip/LASzip.git && \
     cd LASzip && \
-    git checkout tags/3.4.4 && \
     mkdir build && cd build && \
     cmake .. -DCMAKE_BUILD_TYPE=Release && \
     make -j$(nproc) && \
@@ -39,7 +38,6 @@ RUN git clone https://github.com/LASzip/LASzip.git && \
 # Clone, build and clean up Qhull
 RUN git clone https://github.com/qhull/qhull.git && \
     cd qhull && \
-    git checkout tags/v7.3.2 && \
     cd build && \
     cmake .. -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true && \
     make -j$(nproc) && \
@@ -49,7 +47,6 @@ RUN git clone https://github.com/qhull/qhull.git && \
 # Clone, build and clean up libnabo
 RUN git clone https://github.com/ethz-asl/libnabo.git && \
     cd libnabo && \
-    git checkout tags/1.0.7 && \
     mkdir build && cd build && \
     cmake .. -DCMAKE_BUILD_TYPE=RelWithDebInfo && \
     make -j$(nproc) && \
@@ -67,4 +64,4 @@ RUN chmod +x /usr/local/bin/compile_install.sh
 WORKDIR /workspaces/raycloudtools
 
 # Set the default shell to bash
-SHELL ["/bin/bash", "-c"]
+SHELL ["/bin/bash", "-c"]

.devcontainer/commands/compile_install.sh

@@ -5,7 +5,7 @@ set -e
 echo "Building RayCloudTools..."
 cd /workspaces/raycloudtools
 mkdir -p build
-cd build 
+cd build
 
 # Construct the cmake command
 cmake .. \
@@ -41,4 +41,4 @@ make -j"$(nproc)"
 make install
 ldconfig /usr/local/lib
 
-echo "Build process completed successfully."
+echo "Build process completed successfully."

.devcontainer/devcontainer.json

@@ -1,21 +1,30 @@
 {
-    "name": "RayCloudTools Development",
-    "build": {
-        "dockerfile": "Dockerfile",
-        "context": ".."
-    },
-    "customizations": {
-        "vscode": {
-            "extensions": [
-                "ms-vscode.cpptools",
-                "ms-vscode.cmake-tools",
-                "twxs.cmake",
-                "ms-vscode.cpptools-extension-pack"
-            ]
-        }
-    },
-    "remoteUser": "root",
-    "forwardPorts": [],
-    "postCreateCommand": "compile_install.sh",
-    "runArgs": ["--security-opt", "label=disable"]
-}
+  "name": "RayCloudTools Development",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": "..",
+    "options": [
+      "--progress=plain"
+    ]
+  },
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-vscode.cpptools",
+        "ms-vscode.cmake-tools",
+        "ms-vscode.cpptools-extension-pack"
+      ]
+    }
+  },
+  "mounts": [
+    "type=bind,source=${localWorkspaceFolder}/.devcontainer/commands/compile_install.sh,target=/usr/local/bin/compile_install.sh",
+  ],
+  "remoteUser": "root",
+  "forwardPorts": [],
+  "postCreateCommand": "compile_install.sh",
+  "runArgs": [
+    "--security-opt=label=disable"
+  ],
+  "workspaceFolder": "/workspaces/raycloudtools",
+  "workspaceMount": "type=bind,source=${localWorkspaceFolder},target=/workspaces/raycloudtools"
+}

.gitignore

@@ -1,4 +1,4 @@
-.vscode/
 .idea/
 build*/
 cmake-build*/
+treetools/

.vscode/settings.json

@@ -0,0 +1,21 @@
+{
+    "editor.formatOnSave": true,
+    "editor.rulers": [
+        120
+    ],
+    "files.trimFinalNewlines": true,
+    "files.insertFinalNewline": true,
+    "files.trimTrailingWhitespace": true,
+    "C_Cpp.default.cppStandard": "c++20",
+    "C_Cpp.default.cStandard": "c99",
+    "C_Cpp.default.compileCommands": "${workspaceFolder}/build/compile_commands.json",
+    "C_Cpp.files.exclude": {
+        "**/.vscode": true,
+        "build/**": true,
+    },
+    "C_Cpp.exclusionPolicy": "checkFolders",
+    "[cpp]": {
+        "editor.defaultFormatter": "ms-vscode.cpptools",
+        "editor.tabSize": 2
+    }
+}

docker/Dockerfile

@@ -34,7 +34,6 @@ RUN mkdir -p /deps && \
 # Clone, build and clean up LASzip (3.x supports LAS 1.4 via laszip_api.h C API)
 RUN git clone https://github.com/LASzip/LASzip.git && \
     cd LASzip && \
-    git checkout tags/3.4.4 && \
     mkdir build && cd build && \
     cmake .. -DCMAKE_BUILD_TYPE=Release && \
     make -j$(nproc) && \
@@ -97,7 +96,7 @@ RUN git clone https://github.com/csiro-robotics/treetools.git && \
     make install && \
     cd ../.. && \
     rm -rf treetools
-    
+
 # Update ldconfig
 RUN ldconfig /usr/local/lib
 

raycloudtools/raydiff/raydiff.cpp

@@ -17,7 +17,7 @@
 void usage(int exit_code = 1)
 {
   // clang-format off
-  std::cout << "Difference between two ray clouds output a coloured cloud, cloud1 differences in red, cloud2 differences in green, and similarity printed to screen." << std::endl;
+  std::cout << "Difference between two ray clouds output a coloured cloud, cloud1 differences in scarlet, cloud2 differences in green/cyan, and similarity printed to screen." << std::endl;
   std::cout << "usage (--view / -v to view results):" << std::endl;
   std::cout << "raydiff cloud1.ply cloud2.ply" << std::endl;
   std::cout << "                              --distance 0 - optional threshold in m for colouring differences. Default auto-detects distribution shoulder" << std::endl;

raycloudtools/rayimport/rayimport.cpp

@@ -240,4 +240,4 @@ int main(int argc, char *argv[])
   if (save_file != "")
     ray::viewFile(save_file); 
   return res;
-}
+}

raycloudtools/rayinfo/rayinfo.cpp

@@ -74,6 +74,8 @@ int rayInfo(int argc, char *argv[])
   double min_ray_length = std::numeric_limits<double>::max();
   double max_ray_length = std::numeric_limits<double>::lowest();
   double max_bounded_ray_length = std::numeric_limits<double>::lowest();
+  double mean_bounded_ray_length = 0.0;
+  int mean_count = 0;
   ray::RGBA min_col(255, 255, 255, 255), max_col(0, 0, 0, 0);
   int num_pixels_covered = 0;
   const double voxel_width = 0.5;
@@ -125,6 +127,8 @@ int rayInfo(int argc, char *argv[])
       if (colours[i].alpha > 0)
       {
         max_bounded_ray_length = std::max(max_bounded_ray_length, ray_length);
+        mean_bounded_ray_length += ray_length;
+        mean_count++;
 
         min_col.red = std::min(min_col.red, colours[i].red);
         min_col.green = std::min(min_col.green, colours[i].green);
@@ -145,6 +149,7 @@ int rayInfo(int argc, char *argv[])
   {
     usage();
   }
+  mean_bounded_ray_length /= (double)mean_count;
 
   // print the results to screen
   std::cout << std::endl;
@@ -196,7 +201,7 @@ int rayInfo(int argc, char *argv[])
       std::cout << num_minutes << " mins ";
     std::cout << seconds << " s \t(in seconds: " << path_period << ")" << std::endl;
   }
-  std::cout << "  ray length: \t\t" << min_ray_length << " to " << max_ray_length << " m, max end point ray length: " << max_bounded_ray_length << " m" << std::endl;
+  std::cout << "  ray length: \t\t" << min_ray_length << " to " << max_ray_length << " m, max end point ray length: " << max_bounded_ray_length << " m, mean: " << mean_bounded_ray_length << std::endl;
   std::cout << "  colour range (RGBA): \t" << (int)min_col.red << "," << (int)min_col.green << "," << (int)min_col.blue << "," << (int)min_col.alpha << " to " << 
                                             (int)max_col.red << "," << (int)max_col.green << "," << (int)max_col.blue << "," << (int)max_col.alpha << std::endl;
 

raylib/extraction/rayforest_watershed.cpp

@@ -11,6 +11,7 @@
 #include <iostream>
 #include <queue>
 #include "../rayply.h"
+#include "../rayrandom.h"
 
 namespace ray
 {
@@ -39,9 +40,9 @@ void Forest::renderWatershed(const std::string &cloud_name_stub, std::vector<Tre
         continue;
       }
       srand(1 + ind);
-      colour.red = (uint8_t)(rand() % 256);
-      colour.green = (uint8_t)(rand() % 256);
-      colour.blue = (uint8_t)(rand() % 256);
+      colour.red = (uint8_t)(::ray::rand() % 256);
+      colour.green = (uint8_t)(::ray::rand() % 256);
+      colour.blue = (uint8_t)(::ray::rand() % 256);
       Eigen::Vector3d pos =
         min_bounds_ + voxel_width_ * Eigen::Vector3d(0.5 + static_cast<double>(x), 0.5 + static_cast<double>(y), 0);
       pos[2] = original_heightfield_(x, y);
@@ -54,10 +55,10 @@ void Forest::renderWatershed(const std::string &cloud_name_stub, std::vector<Tre
   for (auto &ind : indices)
   {
     Eigen::Vector3d tip;
-    srand(1 + ind);
-    colour.red = (uint8_t)(rand() % 256);
-    colour.green = (uint8_t)(rand() % 256);
-    colour.blue = (uint8_t)(rand() % 256);
+    ::ray::srand(1 + ind);
+    colour.red = (uint8_t)(::ray::rand() % 256);
+    colour.green = (uint8_t)(::ray::rand() % 256);
+    colour.blue = (uint8_t)(::ray::rand() % 256);
     if (trees[ind].area < min_area_)
     {
       continue;

raylib/extraction/raygrid2d.cpp

@@ -203,7 +203,7 @@ void RayIndexGrid2D::init(const Eigen::Vector3d &min_bound, const Eigen::Vector3
             << std::endl;
 
   pixels_.resize(dims_[0] * dims_[1]);
-  memset(&pixels_[0], 0, sizeof(Pixel) * pixels_.size());
+  std::fill(pixels_.begin(), pixels_.end(), Pixel{});
 }
 
 void RayIndexGrid2D::fillRays(const Cloud &cloud)

raylib/extraction/rayleaves.cpp

@@ -10,6 +10,7 @@
 #include "../rayply.h"
 #include "../raymesh.h"
 #include "../rayforeststructure.h"
+#include "../rayrandom.h"
 #define STB_IMAGE_IMPLEMENTATION
 #include "raylib/imageread.h"
 
@@ -144,10 +145,10 @@ bool generateLeaves(const std::string &cloud_stub, const std::string &trees_file
   };
   std::vector<Leaf> leaves;
   std::vector<double> leaf_counter(grid.voxels().size());
-  std::srand(1);
+  ::ray::srand(1);
   for (size_t i = 0; i<grid.voxels().size(); i++)
   {
-    leaf_counter[i] = (double)(std::rand()%10000) / 10000.0; // a random start stops regions of low density have 0 leaves
+    leaf_counter[i] = (double)(::ray::rand()%10000) / 10000.0; // a random start stops regions of low density have 0 leaves
   }
 
 
@@ -170,7 +171,7 @@ bool generateLeaves(const std::string &cloud_stub, const std::string &trees_file
       double num_leaves_d = desired_leaf_area / leaf_area;
       double num_points = (double)voxel.numHits();
       double &count = leaf_counter[index];
-      count += num_leaves_d / num_points;
+      count += num_leaves_d / num_points; 
       bool add_leaf = false;
       if (count >= 1.0)
       {

raylib/extraction/rayterrain.cpp

@@ -9,6 +9,7 @@
 #include "../rayply.h"
 #include "../rayprogress.h"
 #include "../rayprogressthread.h"
+#include "../rayrandom.h"
 
 #if RAYLIB_WITH_TBB
 #include <tbb/enumerable_thread_specific.h>
@@ -49,8 +50,8 @@ struct Node
   {
     num_visits++;
 // This checks in a cone rather than just the corner of a cube shape that you would get
-// from a raw Pareto front calculation    
-#define CONE_CHECK  
+// from a raw Pareto front calculation
+#define CONE_CHECK
     Vector4d dif = corner - pos;
     if (dif == Vector4d(0, 0, 0, 0))
     {
@@ -123,7 +124,7 @@ void constructOctalSpacePartition(std::vector<Node> &nodes, std::vector<Vector4d
   int i = 0;
   while (points.size() > 0)
   {
-    const int ind = rand() % static_cast<int>(points.size());
+    const int ind = ::ray::rand() % static_cast<int>(points.size());
     nodes[i++].pos = points[ind];
     points[ind] = points.back();
     points.pop_back();
@@ -177,7 +178,7 @@ void Terrain::getParetoFront(const std::vector<Vector4d> &points, std::vector<Ve
 #if RAYLIB_WITH_TBB
   tbb::parallel_for<size_t>(0, nodes.size(), process_rays);
 #else
-  #pragma omp parallel for
+#pragma omp parallel for
   for (size_t n = 0; n < nodes.size(); n++)
   {
     process_rays(n);
@@ -200,7 +201,7 @@ void Terrain::getParetoFront(const std::vector<Vector4d> &points, std::vector<Ve
 void Terrain::growUpwards(const std::vector<Eigen::Vector3d> &positions, double gradient)
 {
 #if RAYLIB_WITH_QHULL
-  // The idea behind ground extraction is to tilt the upwards vector to the (1,1,1) direction then 
+  // The idea behind ground extraction is to tilt the upwards vector to the (1,1,1) direction then
   // find the Pareto front in the three principle axes. https://en.wikipedia.org/wiki/Pareto_front
   //
   // Efficient Pareto front calculation is based on: Algorithms and Analyses for Maximal Vector Computation. Godfrey
@@ -255,6 +256,10 @@ void Terrain::growUpwards(const std::vector<Eigen::Vector3d> &positions, double
 
   mesh_.indexList() = hull.mesh().indexList();
   mesh_.vertices() = vecs;
+#else
+  RAYLIB_UNUSED(positions);
+  RAYLIB_UNUSED(gradient);
+  std::cerr << "growUpwards: extracting terrain requires QHull, see README instructions for installation" << std::endl;
 #endif
 }
 
@@ -349,11 +354,20 @@ void Terrain::growUpwardsFast(const std::vector<Eigen::Vector3d> &ends, double p
   std::cout << "size before: " << ends.size() << ", size after: " << points.size() << std::endl;
 
   growUpwards(points, gradient);
+#else
+  RAYLIB_UNUSED(ends);
+  RAYLIB_UNUSED(pixel_width);
+  RAYLIB_UNUSED(min_bound);
+  RAYLIB_UNUSED(max_bound);
+  RAYLIB_UNUSED(gradient);
+  std::cerr << "growUpwardsFast: extracting terrain requires QHull, see README instructions for installation"
+            << std::endl;
 #endif
 }
 
-// Convert the @c cloud input to the mesh_ member variable. 
-void Terrain::extract(const Cloud &cloud, const Eigen::Vector3d &offset, const std::string &file_prefix, double gradient, bool verbose)
+// Convert the @c cloud input to the mesh_ member variable.
+void Terrain::extract(const Cloud &cloud, const Eigen::Vector3d &offset, const std::string &file_prefix,
+                      double gradient, bool verbose)
 {
 #if RAYLIB_WITH_QHULL
   // preprocessing to make the cloud smaller.
@@ -386,6 +400,11 @@ void Terrain::extract(const Cloud &cloud, const Eigen::Vector3d &offset, const s
     local_cloud.save(file_prefix + "_terrain.ply");
   }
 #else
+  RAYLIB_UNUSED(cloud);
+  RAYLIB_UNUSED(offset);
+  RAYLIB_UNUSED(file_prefix);
+  RAYLIB_UNUSED(gradient);
+  RAYLIB_UNUSED(verbose);
   std::cerr << "Error: extracting terrain requires QHull, see README instructions for installation" << std::endl;
 #endif
 }

raylib/extraction/raytrunks.cpp

@@ -9,6 +9,7 @@
 #include "../raycuboid.h"
 #include "../raygrid.h"
 #include "../rayply.h"
+#include "../rayrandom.h"
 #include "raygrid2d.h"
 
 namespace ray
@@ -652,9 +653,9 @@ void Trunks::saveDebugTrunks(const std::string &filename, bool verbose, const st
     for (auto &id : lowest_trunk_ids)
     {
       const Trunk &trunk = trunks[id];
-      colour.red = uint8_t(rand() % 255);
-      colour.green = uint8_t(rand() % 255);
-      colour.blue = uint8_t(rand() % 255);
+      colour.red = uint8_t(::ray::rand() % 255);
+      colour.green = uint8_t(::ray::rand() % 255);
+      colour.blue = uint8_t(::ray::rand() % 255);
 
       const Eigen::Vector3d side1 = trunk.dir.cross(Eigen::Vector3d(1, 2, 3)).normalized();
       const Eigen::Vector3d side2 = side1.cross(trunk.dir);
@@ -725,6 +726,7 @@ std::vector<std::pair<Eigen::Vector3d, double>> Trunks::load(const std::string &
         if (i < 3)
         {
           base[i] = std::stod(token.c_str());
+          radius = 0.0;
         }
         else
         {