hedvis 0.1.1

HED validation, summary, and analysis tools for annotating events and experimental metadata.

HED visualization

hedvis provides word cloud generation and visual summaries for HED-annotated data, making it easy to explore and present the semantic content of your experimental datasets.

Features

• Word Cloud Generation - Create beautiful word clouds from HED tag frequencies
• Flexible Configuration - Extensive customization options for visualizations
• Shaped Clouds - Support for mask images to create custom-shaped word clouds
• Multiple Formats - Export to PNG and SVG formats
• hedtools Integration - Seamless integration with the HED Python tools ecosystem
• Two APIs - A modern configuration-based API (VisualizationConfig) and a simple legacy API for quick tasks

Installation

From PyPI (recommended)

Install the latest stable release:

pip install hedvis

This automatically installs hedtools and all required dependencies.

Development installation

For development work, clone the repository and install in editable mode:

git clone https://github.com/hed-standard/hed-vis.git
cd hed-vis
pip install -e .

Installing optional dependencies

The project uses pyproject.toml as the single source of truth for all dependencies. Install optional dependencies using pip extras.

Important: Installing with extras automatically includes all base dependencies (hedtools, numpy, pandas, etc.) plus the extra tools.

Development tools (code formatting, linting, testing):

# From PyPI (if you installed hedvis from PyPI)
pip install "hedvis[dev]"

# From local source (if you cloned the repository)
pip install ".[dev]"          # Regular install
pip install -e ".[dev]"       # Editable install (recommended for development)

Documentation tools (Sphinx, themes):

# From PyPI
pip install "hedvis[docs]"

# From local source
pip install ".[docs]"

Both dev and docs dependencies:

# From PyPI
pip install "hedvis[dev,docs]"

# From local source
pip install ".[dev,docs]"

Installing from source without extras

To install from source with only the core dependencies:

git clone https://github.com/hed-standard/hed-vis.git
cd hed-vis
pip install .

If you need to install dependencies for development or documentation:

• Use pip install ".[dev]" instead of pip install -r requirements-dev.txt
• Use pip install ".[docs]" instead of pip install -r docs/requirements.txt
• Core dependencies are installed automatically with pip install . or pip install hedvis

Quick start

Simple word cloud

from hedvis import create_wordcloud

# Create word cloud from frequency dictionary
word_freq = {
    "Event": 15,
    "Action": 10,
    "Sensory-event": 8,
    "Visual-presentation": 7
}

wc = create_wordcloud(word_freq, width=800, height=600)
wc.to_file("wordcloud.png")

Using the hedvis API

from hedvis import HedTagVisualizer, WordCloudConfig, VisualizationConfig

# Configure visualization
wc_config = WordCloudConfig(
    width=1200,
    height=800,
    background_color="white",
    colormap="viridis"
)

viz_config = VisualizationConfig(
    word_cloud=wc_config,
    output_formats=["png", "svg"]
)

# Create visualizer
visualizer = HedTagVisualizer(viz_config)

# Generate from HED tag counts (from hedtools)
results = visualizer.visualize_from_counts(tag_counts)

Integration with hedtools

from hed import load_schema
from hed.models import TabularInput
from hedvis import HedTagVisualizer

# Load HED schema and data
schema = load_schema()
tabular = TabularInput("events.tsv", sidecar="events.json")

# Create visualizer
visualizer = HedTagVisualizer()

# Generate visualizations
results = visualizer.visualize_from_tabular(
    tabular,
    schema,
    output_basename="experiment_tags"
)

# Save word cloud
results['word_cloud']['wordcloud_object'].to_file("tags.png")

All dependencies are managed in pyproject.toml and installed automatically with pip install hedvis.

For the complete list of dependencies with exact versions, see the dependencies section in pyproject.toml.

Development setup

Prerequisites

• Python 3.10 or higher
• Git
• pip (Python package manager)

Setting up your development environment

1. Fork and clone the repository:

   git clone https://github.com/YOUR_USERNAME/hed-vis.git
   cd hed-vis
   

2. Create a virtual environment (recommended):

   python -m venv .venv
   .venv\Scripts\activate  # On Windows PowerShell
   source .venv/bin/activate  # On Unix/MacOS
   

3. Install in development mode:

   All dependencies are managed in pyproject.toml. Install the package with development tools:

   pip install -e ".[dev]"
   

   This installs:

   • The hedvis package in editable mode
   • All required dependencies (hedtools, wordcloud, matplotlib, etc.)
   • Development tools (black, ruff, codespell, mdformat)
   • Testing tools (coverage)

   To install additional optional dependencies:

   # Documentation tools
   pip install -e ".[docs]"
   
   # Both dev and docs
   pip install -e ".[dev,docs]"
   

   Note: Do not use legacy requirements files (requirements.txt, requirements-dev.txt). All dependencies are defined in pyproject.toml.

4. Run tests to verify setup:

   python -m unittest discover tests
   

Related projects

• hedtools - Core HED tools for validation and analysis
• hed-schemas - Official HED schemas
• hed-specification - HED specification
• table-remodeler - Sister project with table manipulation tools

Contributing

Contributions are welcome! Please see CONTRIBUTING.md for guidelines.

Support

• HED homepage: https://www.hedtags.org
• Repo docs: https://www.hedtags.org/hed-vis
• GitHub issues: https://github.com/hed-standard/hed-vis/issues
• Ideas or questions: https://github.com/orgs/hed-standard/discussions
• HED Homepage: https://www.hedtags.org
• Contact: [e-mail]

License

This project is licensed under the MIT License - see LICENSE for details.

Citation

If you use hedvis in your research, please cite:

If you use HEDTools in your research, please cite:

@software{hedtools,
  author = {Ian Callanan, Robbins, Kay and others},
  title = {HEDVis: Visualization tools for HED},
  year = {2024},
  publisher = {GitHub},
  url = {https://github.com/hed-standard/hed-vis},
}