substrata

Getting Started

  • Installation
    • Quick Start
    • Requirements
  • Command-line usage of substrata
    • Decimation of PLY files
    • PLY file preview (head)
    • Visual assessment of scalebars
    • Composite views
    • Orientation and scaling
    • FireFish alignment
    • Camera video creation
    • Z-intercepts calculation
    • Point cloud alignment
    • Image matches
    • Classifier training

Tutorials

  • Scaling and orientation with substrata
    • Loading a point cloud
    • Scaling the point cloud
    • Orientation
  • Transferring 3D annotations between different reconstructions of the same pointcloud
    • Loading in the old annotations and exporting image matches
    • Loading in the new pointcloud and camera files and importing the old annotations based on 2D image coordinates
  • Topographic position index (TPI) and terrain ruggedness index (TRI)
    • Load in the pointcloud and annotations and scale/orient using predefined saved world transform
    • Prepare for measurements and visualizations
    • Calculate and visualize topographic position index (TPI) and terrain ruggedness index (TRI)
    • Different parameter options
    • Comparison of different parameter options - different neighborhood size (=annulus width)
    • Comparison of different parameter options - z or mean z from inner
    • Comparison of different parameter options - rasterization
    • Comparison of different parameter options - with or without coral colony
    • Comparison with roughness parameter

API Reference

  • API Reference
    • Core Modules
    • Analysis and Processing
    • Visualization
    • Configuration and Utilities
      • setup_logging()
      • tqdm_joblib()
    • Command Line Interface
substrata
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