HabiCAT 3D
Habitat Complexity Analysis Tool 3D

HabiCAT 3D is an open-source software that implements novel algorithms for generating multi-scale complexity metrics maps(like rugosity, fractal dimension, vector dispersion and others) for complex 3D habitat models. It extends traditional complexity metrics calculations to fully capture the three-dimensional complexity of real-world environments. Designed for ecologists and researchers, this tool facilitates the analysis, export and visualization of 3D habitat models, particularly coral reefs, and other complex structures.

• Multi-Scale Maps: Generates detailed maps over varying scales to capture the intricate details of complex models.

• Complexity Metrics Available to Calculate:

  • Rugosity:
    • Average Normal(default): The simplest and fastest way to calculate rugosity, but for more acurate results, we highly recommend using "Min Rugosity".
    • Optimized Reference Planes(Min Rugosity): A rugosity-minimizing technique for accurate reference plane selection, improving calculation accuracy.
    • Unique Projected Area: To correctly calculate rugosity on very complex models, users can opt to use this option. Currently, it is very slow, but we plan to improve its performance in the future.
  • Fractal Dimension.
  • Vector Dispersion.
  • Triangle Area.
  • Triangle Density.

• Layers: Our layer system allows users to compare results obtained using different metrics and settings. Each analysis run creates a new layer, which can be accessed through tabs at the top of the screen. Users can visually compare layers or generate heatmaps to highlight the differences between them.

• .RUG file format: Users can save and load entire workspace using a custom (.RUG) format. RUG files save all layers alongside the model, decreasing model load times and eliminating the need to re-run calculations.

• Histograms: Interactive histograms provide deeper insight into the distribution of complexity metrics across the model. At a glance, it is possible to quickly evaluate the uniformity or concentration of complexity in a model.

  • Histogram selection: Histograms can be queried by mouse to calculate how much surface area falls within a complexity range. Regions corresponding to selected ranges are highlighted to aid correlating the histogram to the model:

• CLI Scripting: The application supports a command-line interface (CLI) and script execution without a graphical user interface (GUI), allowing for streamlined integration into existing researchers' workflows.

• Export Options:

  • Selection tool (Only in GUI Mode): The user can query the layer value of a single triangle or the layer values within a specified radius of a point. If the 'Export to File' option is activated, then the values will be automatically saved to a text file.
  • Screenshot (Only in GUI Mode): The 'Take Screenshot' button generates a screenshot without the GUI and with a larger legend, making it suitable for use in figures.
  • Whole Layer as Image: Layer values will be projected onto a plane and converted to a PNG or GeoTIFF (color or 32-bit float with raw values) image. The 32-bit float raw export is essential for easy use of the application's calculation results in other applications.
    • Cumulative Suboption: In complex 3D models, multiple triangles may project to the same pixel when creating a 2D image. The cumulative option resolves this by accumulating the complexity metric along the projection axis, creating an "X-ray" effect that preserves information about high-complexity areas. This option is useful for models with overhangs and caves.

Quick start guide for GUI mode.

Quick start guide for CLI mode.

• Download ready-to-use application:
• Download source code and compile: Look for instructions below.

The compilation process was tested with Windows 10 (and 11) and Visual Studio 2022. To compile, you would need Git, CMake, and Visual Studio.

# Initialize a new Git repository
git init

# Add the remote repository
git remote add origin https://github.com/Azzinoth/HabiCAT3D

# Pull the contents of the remote repository
git pull origin master

# Initialize and update submodules
git submodule update --init --recursive

# Generate the build files using CMake
# CMake should be added to a PATH
# if not then use CMAKE GUI
cmake CMakeLists.txt

After running these commands, you should have a Visual Studio project that is ready to be compiled.

This project uses the following third-party libraries:

1. Focal Engine: This library is licensed under MIT License. The full license text can be found at Focal Engine's GitHub repository
2. CGAL: Some parts of CGAL are available under the LGPL, whereas other parts are under the GPL. The full license text can be found at CGAL's GitHub repository or CGAL's webpage.
3. boost: This library is licensed under Boost Software License. The full license text can be found at boost's GitHub repository
4. Eigen: This library is part of CGAL.
5. GDAL: This library is licensed under MIT License. The full license text can be found at GDAL's GitHub repository