TIMESAT CLI

TIMESAT CLI is a command line interface and workflow manager for the TIMESAT package. It provides a convenient way to configure and execute TIMESAT processing pipelines directly from the command line or automated scripts.

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Requirements

Before you begin, make sure you have:

• Miniconda or Anaconda (for environment management)
  Download: https://docs.conda.io/en/latest/miniconda.html
• Python 3.10+

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Installation

timesat-cli is available on PyPI and can be installed using pip or uv.
Although it is not published on Conda, you can safely install it inside a Conda environment.

Option 1 — Install inside a Conda environment

conda create -n timesat-cli python=3.12
conda activate timesat-cli
pip install timesat-cli

This approach uses Conda only for environment isolation.
The installation itself is handled by pip, which will automatically install timesat and all required dependencies.

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Option 2 — Install via uv (recommended for pure Python environments)

uv is a modern, high-performance alternative to pip and venv.

1. Install uv:

   pip install uv
   # or
   curl -LsSf https://astral.sh/uv/install.sh | sh

2. Create a virtual environment and install the package:

   uv venv .venv
   source .venv/bin/activate
   uv pip install timesat-cli

uv provides faster dependency resolution and caching.
It will automatically install timesat and related dependencies.

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Option 3 — Direct installation with pip

If you already have Python 3.10+ installed:

pip install timesat-cli

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⚙️ Optional: Parallel Processing Support

timesat-cli provides an optional extra for parallel execution using ray.

To install with parallel-processing support:

pip install timesat-cli[parallel]

This installs the base package plus the ray dependency.

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Running the Application

After installation, start the GUI with:

timesat-cli path/to/settings.json

or equivalently:

python -m timesat_cli path/to/settings.json

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Advanced Usage

If you wish to customize or extend the workflow, you can also run or modify the main script directly:

python timesat_run.py

The file 'timesat_run.py' contains the full example pipeline that invokes core modules from the 'timesat_cli' package, including configuration loading, file management, TIMESAT processing, and output writing.

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HRVPP Notes — QFLAG2 weights

If you work with HRVPP quality flags (QFLAG2), the following weights w are commonly applied:

QFLAG2 value	Weight w
1	1.0
4097	1.0
8193	1.0
12289	1.0
1025	0.5
9217	0.5
2049	0.5
6145	0.5
3073	0.5

Example (settings.json):

"p_a": {
  "value": [
    [1, 1.0],
    [4097, 1.0],
    [8193, 1.0],
    [12289, 1.0],
    [1025, 0.5],
    [9217, 0.5],
    [2049, 0.5],
    [6145, 0.5],
    [3073, 0.5]
  ],
  "description": "QA weighting rules. Leave empty [] to keep original QA values. Use [qa_value, weight] for exact matches or [min, max, weight] for ranges."
}

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License

TIMESAT-CLI is released under the GNU General Public License (GPL).
You are free to use, modify, and distribute this software under the terms of the GPL.

The GPL license applies only to the TIMESAT-CLI source code and assets provided in this repository.

📦 Dependency Licenses

• timesat may install additional open-source dependencies (e.g., Flask, pandas, NumPy).
• Each dependency retains its own license (MIT, BSD, Apache, etc.).
• Before redistributing or bundling this software, review the license terms of each dependency carefully.

⚖️ Summary

Component	License Type	Notes
TIMESAT-CLI	GPL v3	Open source, modification and redistribution permitted under GPL.
TIMESAT	Proprietary	All rights reserved. Redistribution and modification prohibited without written consent.
Other Dependencies	Various (MIT/BSD/Apache)	Check individual package licenses before redistribution.

For detailed license information, refer to the license files distributed with each installed package.

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Citation

If you use TIMESAT, TIMESAT-CLI or TIMESAT-GUI in your research, please cite the corresponding release on Zenodo:

Cai, Z., Eklundh, L., & Jönsson, P. (2025). TIMESAT4: is a software package for analysing time-series of satellite sensor data (Version 4.1.x) [Computer software]. Zenodo.
https://doi.org/10.5281/zenodo.17369757

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Acknowledgments

• TIMESAT — Original analysis framework for satellite time-series data.
• This project acknowledges the Swedish National Space Agency (SNSA), the European Environment Agency (EEA), and the European Space Agency (ESA) for their support and for providing access to satellite data and related resources that made this software possible.

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