H5forest

A Text-based User Interface (TUI) for exploring HDF5 files

h5forest brings interactivity and new functionality to HDF5 file exploration. Unlike traditional command-line tools like h5ls or h5glance, h5forest provides a fully interactive terminal interface for navigating complex HDF5 file hierarchies.

Features

• Interactive Interface: Handle large files with deep hierarchies through an intuitive TUI
• Real-time Displays: Live metadata and attribute views that update as you navigate
• Modal System: Vim-like modal interface for different interaction modes
• Lazy Loading: Efficient handling of large datasets with chunked data support
• Dataset Inspection: Peek inside datasets with automatic truncation for large arrays
• Statistical Analysis: Compute statistics (min/max, mean, standard deviation) on the fly
• Data Visualization: Generate quick scatter plots and histograms
• Asynchronous Operations: Responsive interface that doesn't block during heavy computations
• Fuzzy Search: Quickly find datasets and groups with real-time filtering
• Fully customisable: Tailor the interface and functionality using a simple configuration file

Basic Installation And Usage

Install h5forest via pip:

pip install h5forest

Then explore any HDF5 file:

h5forest /path/to/your/file.hdf5

Navigation Overview

h5forest uses a modal interface with different modes for different tasks:

• Normal Mode: Default navigation and tree exploration
• Search Mode: Fuzzy search to quickly find datasets and groups
• Jump Mode: Quick navigation commands
• Dataset Mode: Data analysis and statistics
• Window Mode: Panel and focus management
• Plotting Mode: Create scatter plots from data
• Histogram Mode: Generate histograms and distributions

Use keyboard shortcuts to switch between modes and perform actions. Press q to exit any mode or the application.

Documentation Sections

• Getting Started: Installation and basic setup
• Quick Start: Get up and running in minutes
• Mode Reference: Detailed guide to all interaction modes
• Configuration: Customizing h5forest to your needs
• Contributing: Development setup and contribution guidelines
• FAQ: Common questions and troubleshooting

Why h5forest?

Traditional HDF5 tools work well for quick inspections, but h5forest excels when you need to:

• Explore complex, deeply nested file structures
• Interactively analyze datasets without writing scripts
• Generate quick visualizations during data exploration
• Navigate large files efficiently with lazy loading
• Perform statistical analysis on datasets of any size

Community

h5forest is developed by Will Roper.

Get Involved:

• Contribute: See our Contributing Guide for development setup and guidelines
• Report Issues: Submit bug reports and feature requests on GitHub Issues
• Discussions: Join conversations on GitHub Discussions
• Source Code: Fork and star the project on GitHub

License

h5forest is released under the GPL v3 License. See the LICENSE file for details.